Molecular Data Provider
We developed MolePro, a knowledge-centric data provider for systems chemical biology, as part of the NCATS Biomedical Data Translator (“Translator”). MolePro aims to (1) integrate data sources in an unbiased way, and (2) provide a curated, unified framework for chemical entities to deepen our understanding of target biology. MolePro takes advantage of broad access to a powerful and diverse suite of public chemical-biology datasets, portals, and tools, to integrate information available for compounds and their protein targets, including similarity-based connections. We follow a stringent procedure to avoid expert bias, including data scouting, architecture building, and capturing data provenance, to create a unified framework for compounds and their targets that can suggest new compounds or new targets based on “guilt-by-association” inferences from large data corpora. We bring to the Translator project chemical-biology expertise that typically involves probe- or drug-discovery activities, flagging toxicity or other unwanted effects, and highlighting small-molecule mechanisms of action.
Vlado Dancik (@vdancik)
We have made MolePro's knowledge graph available to the scientific community via API hosted on an NCATS Translator server, https://molepro.transltr.io/molecular_data_provider/api
as well as on a Broad Institute server: https://translator.broadinstitute.org/molecular_data_provider/api
https://translator.broadinstitute.org/molepro/trapi/v1.5/ui/
- BiGG Models http://bigg.ucsd.edu/
- BigGIM http://biggim.ncats.io/api/
- BindingDB https://www.bindingdb.org/
- ChEBI https://www.ebi.ac.uk/chebi
- ChemBank http://chembank.broadinstitute.org/
- ChEMBL https://www.ebi.ac.uk/chembl/
- CMAP https://clue.io/
- CTD http://ctdbase.org/
- CTRP http://portals.broadinstitute.org/ctrp/
- DepMap https://depmap.org/portal/
- DGIdb http://dgidb.org/
- DrugBank https://www.drugbank.ca/
- DrugCentral http://drugcentral.org/privacy
- Drug Repurposing Hub https://clue.io/repurposing
- Gelinea https://github.com/broadinstitute/GeLiNEA
- GtoPdb https://www.guidetopharmacology.org/
- HGNC https://www.genenames.org
- HMDB https://www.hmdb.ca/
- Inxight:Drugs https://drugs.ncats.io/
- Kinomescan https://lincs.hms.harvard.edu/kinomescan/
- MSigDB https://www.gsea-msigdb.org/gsea/msigdb/index.jsp
- PharmGKB https://www.pharmgkb.org/
- Pharos https://pharos.nih.gov
- ProbeMiner https://probeminer.icr.ac.uk/#/
- PubChem https://pubchem.ncbi.nlm.nih.gov/
- RxNorm https://www.nlm.nih.gov/research/umls/rxnorm/index.html
- SIDER http://sideeffects.embl.de/
- STITCH http://stitch.embl.de
- STRING https://string-db.org/
For additional details about ingested data source see Catalog of MolePro knowledge sources (JSON formatted output).
